Table 1.
Structures of the three types of datasets used in this study.
Fig 1.
Characteristics of genotypes in Chinese Holstein cattle.
A) The distribution of the Minor Allele Frequency (MAF). All the SNPs with MAF < 0.05 were removed from the analysis. For the remaining SNPs, frequency increases incrementally with increasing MAF. B) The heterozygous rate distribution. Most of the SNPs have a medium rate of heterozygous. The heterozygous rate of about 50% exhibited the highest frequency. C) Linkage disequilibrium (LD) change by marker distance. The average LD between two markers with a distance of less than 10 kb is more than 0.6. R-square decreased quickly with increasing marker distance. D) The average marker distance in the 30 bovine chromosomes. Chromosome 1–29 are autosomes; X is the sex chromosome. The average marker distance in all autosomes is about 50 kb. The marker distance in the sex chromosome is almost 100 kb.
Table 2.
Statistics for adjusted measurements of 38,602 individuals at 6, 12, 18, and 24 months after birth.
Table 3.
Heritabilities, genetic and phenotypic correlations for Heart Girth (HG) and Hip Height (HH) in Chinese Holstein.
Fig 2.
Results of the genome-wide association studies.
The strengths of genome-wide association studies (GWAS) are illustrated by the Manhattan plots on the left panel. The deviations of the signals from null hypothesis are illustrated as the Quantile-Quantile (QQ) plots on the right panel. The negative logarithms of the observed (y axis) and the expected (x axis) P values are plotted for each SNP (dot). GWAS were performed on HG and HH at age of 6, 12, 18, and 24 months separately. Each analysis is labeled as trait (HG or HH) and month on the far right. The number neighboring each trait indicates the age of measurement (e.g., HG6 = Heart Girth at 6 months). The dependent variables were the estimated breeding values (EBVs) calculated from 3,325 individuals, which were genotyped with 42,307 SNPs. The horizontal red lines on the Manhattan plots are the Bonferroni multiple test threshold corresponding type I error of 1%. The red lines on the QQ plots indicate the null hypothesis of no true association. Deviation from the expected P-value distribution is evident only in the tail area for each trait, suggesting that population stratification was adequately controlled. In total, these GWAS identified 27 SNPs significantly associated with HG and HH. The genes listed at the top of the Manhattan plots are reported as known genes which are highly related to growth or body size traits.
Table 4.
Significant SNPs identified for Heart Girth (HG) and Hip Height (HH) in Chinese Holstein.
Table 5.
List of candidate genes associated with Heart Girth (HG) and Hip Height (HH) in Chinese Holstein.
Fig 3.
The related genes and their network with candidate genes.
The network was constructed based on 16 candidate genes identified in current study by using Ingenuity Pathway Analysis (IPA) software. The IPA score was set at 34 for relating to cell cycle, connective tissue development and function, developmental disorder. The 16 candidate genes from current study were marked into grey, while the 18 white nodes are relevant transcription factors identified by IPA algorithm. Solid and dashed lines indicated direct interaction and indirect interaction, respectively. Genes are presented as nodes and their relationship are presented as edges. The functions of genes are illustrated by the shape of the node. The types of the relationship are illustrated by the ending shapes of the edges.